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to stay on topic.. i always thought the shade mind thingy when extracting bijuu.. the one of the leader does not match peins face... the shape of the head looks different and of the hair, and why do people keep makin pein with red eyes, in naruto shippuuden you can see he has light tinted blue eyes...

Shippuden is just the anime. They wouldn't know either way, so they just do whatever until it's made official. I don't watch the anime, but I'm pretty sure whatever your referring to was in the anime before he was actually shown in the manga. Manga>Anime.

I started thinking that Pein may be the AL because of his strategy and intelligence, but if Oda have kept still another character in the shadows and haven't told us the name of BH... won't those two characters be even stronger than Pein?

That's the usual way Kishimoto reveals the characters (and all the other shonens...).